Abdo Lab

The Abdo lab is interested in studying the microbiome, its interactions and function, and how it interacts with and affects its hosts’ health and is affected by its surrounding environment. This specifically includes studying the relationship between host immune system and the microbiome as it is influenced by external perturbations including vaccination, prebiotics, probiotics, antibiotics and other factors such as viral, or other, infections. This is in addition studying viral evolution and plasmid transfer and evolution as it impacts acquisition, transmission and maintenance of antimicrobial resistance. Another interest of the Abdo Lab is focused on developing and applying computational tools for processing and analysis of high throughput sequence data, and the associated metadata, in addition to developing inferential and predictive models and machine learning methods to facilitate understanding of these complex biological systems.

Some of the software generated through the Abdo lab is available on Github: https://github.com/Abdo-Lab.

The Abdo lab is part of the CSU Microbiome Network.

research project

Mucosal Immunity and the Microbiome

Challenge: Little is known about changes in the gut microbiome during vaccination, especially with an oral-probiotic vector.

Objective: Evaluate use of Lactobacillus acidophilus as a probiotic vaccine vector and the reciprocal interactions between the host’s immune response and alterations in the gut microbiome.

research project

Antimicrobial Resistance and the Microbiome

Challenge: Little is known about antimicrobial resistance reservoirs in natural environments, especially in food production. Hard to link mobile genetic elements to host microbes.

Objective: Examine the impact of both limiting and removing antibiotic use on the resistome and antimicrobial resistance evolution in poultry (food) production.

research project

Viral Ecology and Evolution

Challenge: Whole Genome Sequencing of AIV provides a faster more accurate approach and removes need for propagation in chicken eggs for AIV diagnostics.

Objective: Evaluate impact of virus isolation on virus mutation, natural selection, reassortment, and detection of co-infections.

research project

Methods for Metagenomics Classification and Modeling

Challenge: Large data sets are generated using high throughput sequencing and scalable computational tools to process and classify these data are lacking.

Objective: Develop a fast and accurate classification method for high throughput shotgun metagenomics data utilizing Low-Density Parity-Check and Naïve Bayes Classifier implemented using GPU computing.

Publications

Population genomic transformations induced by isolation of wild bird avian influenza viruses (Orthomyxoviridae) in embryonated chicken eggs

Hopken M, Piaggio A, Pabilonia K, Pierce J, Anderson T, Pierce C, Abdo Z. 2020.
https://doi.org/10.1016/j.meegid.2020.104505

Impact of oral probiotic Lactobacillus acidophilus vaccine strains on the immune response and gut microbiome of mice

Z Abdo, J LeCureux, A LaVoy, B Eklund, EP Ryan, GA Dean. 2019.
PloS one 14 (12), e0225842

Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis

N Noyes, KC Cho, J Ravel, LJ Forney, Z Abdo. 2018.
PLoS One 13 (1), e0191625

Fast maximum likelihood estimation and supervised classification for the Beta-Liouville Multinomial.

Lakin, S. M. and Z. Abdo. 2020.
arXiv:2006.07454

Reads2Resistome: an adaptable and high-throughput whole-genome sequencing pipeline for bacterial resistome characterization. 

Woyda, R., A. Oladeinde, Z. Abdo. 2020.
BioRxiv, doi: https://doi.org/10.1101/2020.05.18.102715

more publications

People

Zaid Abdo, Ph.D.

Lab Principal Investigator [PI]
Associate Professor
Associate Department Head for Graduate Studies

Steven Lakin, D.V.M.

Graduate Research Assistant

Reed Woyda, M.S.

Graduate Research Assistant

Darby Gilfillan

Graduate Research Assistant

Bridget Eklund

Graduate Research Assistant

Crystal Wiersma

USDA ORISE Fellow

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contact information

Lab: Research Innovation Center (RIC) room D139

Office: Research Innovation Center (RIC) room D114

(970) 492-4455